+++ /dev/null
-/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
-
-/*********************************************************************
- * Clustal Omega - Multiple sequence alignment
- *
- * Copyright (C) 2010 University College Dublin
- *
- * Clustal-Omega is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License as
- * published by the Free Software Foundation; either version 2 of the
- * License, or (at your option) any later version.
- *
- * This file is part of Clustal-Omega.
- *
- ********************************************************************/
-
-/*
- * RCS $Id: hhhitlist.h 243 2011-05-31 13:49:19Z fabian $
- */
-
-// hhhitlist.h
-
-//////////////////////////////////////////////////////////////////////////////
-// HitList is a list of hits of type Hit
-// which can be operated upon by several anaylsis methods
-//////////////////////////////////////////////////////////////////////////////
-class HitList : public List<Hit>
-{
-private:
- double score[MAXPROF]; // HHsearch score of each HMM for ML fit
- double weight[MAXPROF]; // weight of each HMM = 1/(size_fam[tfam]*size_sfam[hit.sfam]) for ML fit
- int Nprof; // Number of HMMs for ML fit
-
-public:
- int fams; // number of families found found in hitlist
- int sfams; // number of superfamilies found in hitlist
- int N_searched; // number of sequences searched from HMM database
- Hash<float>* blast_logPvals;/* Hash containing names and log(P-values)
- read from BLAST file (needed for HHblast) */
-
- HitList() {blast_logPvals=NULL;}
- ~HitList() {if (blast_logPvals) delete blast_logPvals;}
-
- // Print summary listing of hits
- void PrintHitList(HMM& q, char* outfile);
-
-#ifdef CLUSTALO
- void ClobberGlobal(void);
-#endif
-
- // Print alignments of query sequences against hit sequences
- int PrintAlignments(
-#ifdef CLUSTALO
- char **ppcFirstProf, char **ppcSecndProf,
-#endif
- HMM& q, char* outfile, char outformat=0);
-
- // Return a figure of merit for distinction of the score with positive from the scores with negatives
- void Optimize(HMM& q, char* buffer);
-
- // Print score distribution into file score_dist
- void PrintScoreFile(HMM& q);
-
- // Log likelihood for fitting the EVD to the score distribution
- double RankOrderFitCorr(double* v);
- // Static wrapper-function for calling the nonstatic member function RankOrderFitCorr()
- static double RankOrderFitCorr_static(void* pt2hitlist, double* v);
-
- // Log likelihood for fitting the EVD to the score distribution
- double LogLikelihoodCorr(double* v);
- // Static wrapper-function for calling the nonstatic member function LogLikelihoodCorr()
- static double LogLikelihoodCorr_static(void* pt2hitlist, double* v);
-
- // Log likelihood for fitting the EVD to the score distribution
- double LogLikelihoodEVD(double* v);
- // Static wrapper-function for calling the nonstatic member function LogLikelihoodEVD()
- static double LogLikelihoodEVD_static(void* pt2hitlist, double* v);
-
-
- // Subroutine to FindMin: new point given by highest point ihigh, fac and replaces ihigh if it is lower
- double TryPoint(int ndim, double* p, double* y, double* psum, int ihigh, double fac, double (*Func)(void* pt2hitlist, double* v));
-
- // Find minimum with simplex method of Nelder and Mead (1965)
- float FindMin(int ndim, double* p, double* y, double tol, int& nfunc, double (*Func)(void* pt2hitlist, double* v));
-
- // Do a maximum likelihood fit of the scores with an EV distribution with parameters lamda and mu
- void MaxLikelihoodEVD(HMM& q, int nbest);
-
- // Calculate correlation and score offset for HHblast composite E-values
- void CalculateHHblastCorrelation(HMM& q);
-
- // Calculate HHblast composite E-values
- void CalculateHHblastEvalues(HMM& q);
-
- // Calculate Pvalues as a function of query and template lengths and diversities
- void CalculatePvalues(HMM& q);
-
- // Set P-values, E-values and scores according to q.lamda and q.mu (if calibration from database scan is impossible)
- void GetPvalsFromCalibration(HMM& q);
-
- // HHblast: read PSI-BLAST E-values to determine correlation
- void ReadBlastFile(HMM& q);
-
- // Print first 20 hits of hitlist
- void Debug()
- {
- Hit hit;
- int i=0;
- Reset();
- printf("TARGET FAMILY LEN COL LOG-PVA S-AASS PROBAB SCORE_SORT\n");
- while (++i<=20 && !End())
- {
- hit = ReadNext();
- printf("%-10.10s %-10.10s %3i %3i %s %7.2f %6.2f %6.2f\n",hit.name,hit.fam,hit.L,hit.matched_cols,sprintg(-1.443*hit.logPval,7),-hit.score_aass,hit.Probab,hit.score_sort);
- }
- }
-
- // Calculate P-values and Probabilities from transitive scoring over whole database
- void TransitiveScoring();
- void TransitiveScoring2();
- void TransitiveScoring3();
- void TransitiveScoring4();
-
- // Score2Z transforms the -log(P-value) score into a Z-score for 0 < S
- double Score2Z(double S);
-
- // Z2Score transforms the Z-score into a -log(P-value) value
- double Z2Score(double Z);
-
- // Matrix manipulation
- void PrintMatrix(float** V, int N);
- void PrintMatrix(double** V, int N);
- float NormalizationFactor(double** Csub,float* w, int M);
- void Normalize(float* Ztq, char** fold, Hash<int>& excluded);
- void InvertMatrix(double** B, double** A, int N);
- void TransposeMatrix(double** V, int N);
- void SVD(double **A, int n, double w[], double **V);
-
-};
-
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